Soto-Cerda B.J.,Agri aquaculture Nutritional Genomic Center |
Carrasco R.A.,Austral University of Chile |
Aravena G.A.,Agri aquaculture Nutritional Genomic Center |
Urbina H.A.,Agri aquaculture Nutritional Genomic Center |
Navarro C.S.,Agri aquaculture Nutritional Genomic Center
Plant Molecular Biology Reporter | Year: 2011
One of the major concerns in genetic characterization and breeding of cultivated flax is the lack of informative microsatellite markers (SSRs). In this regard, the development of SSRs using molecular methods might be time-consuming, laborious, and expensive. On the other hand, using bioinformatics to mine sequences in public databases enables a cost-effective discovery of SSRs. A total of 3,242 Linum usitatissimum genomic sequences were surveyed for the identification of SSRs. Among them, 118 non-redundant sequences containing repeats were selected for designing primers. The most abundant motifs were tri- (72.4%) and dinudeotide (16.6%), within which AGG/CCT and AG/CT were predominant. Primers were tested for polymorphism in 60 L. usitatissimum cultivars/accessions including 57 linseed and three fiber flax. Eighty-eight pairs gave amplifications within the expected size range while 60 pairs were found to be polymorphic. The mean number of alleles amplified per primer was 3.0 (range, 2-8; 180 total alleles). The mean polymorphism information content (PIC) value was 0.39 (range, 0.06-0.87), and the highest average PIC was observed in dinucleotide SSRs (0.41). The SSR data mining presented here demonstrates the usefulness of in silico development of microsatellites. These novel genomic SSR markers could be used in genetic diversity studies, the development of genetic linkage maps, quantitative trait loci mapping, association mapping, and marker-assisted selection. © 2010 Springer-Verlag.
Havananda T.,Cornell University |
Brummer E.C.,University of Georgia |
Maureira-Butler I.J.,Agri Aquaculture Nutritional Genomic Center |
Doyle J.J.,Cornell University
Systematic Botany | Year: 2010
The Medicago sativa species complex includes tetraploid cultivated alfalfa and several other diploid and tetraploid taxa that are recognized either as subspecies of M. sativa or as separate species. The two principal diploid taxa are "caerulea," with purple flowers and coiled pods, and "falcata" with yellow flowers and falcate pods. To understand the evolutionary relationships among taxa in the complex, sequence variation in two noncoding regions of cpDNA (rpl20-rps12 and tmS-tmG spacers) and three regions of mitochondrial DNA (mtDNA: nad4 intron, nad7 intron, and rpS14-cob spacer) were surveyed from 48 (37 for mtDNA) individuals representing these and other diploid taxa in the complex. These sequences afforded independent perspectives on the evolutionary history of the group, because mtDNA is maternally inherited in Medicago whereas cpDNA is biparentally inherited with strong paternal bias. Twenty and 21 haplotypes were identified for cpDNA and mtDNA, respectively. Haplotype networks were constructed and tests of differentiation were conducted. Results from cpDNA sequences supported the recognition of "caerulea" and "falcata" as differentiated taxa, despite the presence of some shared haplotypes, in agreement with morphological characters. In contrast, no significant evidence of mtDNA haplotype differentiation was observed. Incongruence between cpDNA and mtDNA is more likely explained by introgression of the mitochondrial genome than by incomplete lineage sorting of mtDNA haplotypes, given the expected smaller effective population size for uniparentally inherited mtDNA than for biparentally inherited cpDNA. Moreover, the two taxa are readily crossable, making natural hybridization possible. The long-time disagreement on whether to recognize "falcata" as a separate species or a subspecies of M. sativa s. 1. is due to the common problem of unequal rates of differentiation for different characters during speciation. © Copyright 2010 by the American Society of Plant Taxonomists.
Snowdon R.J.,Justus Liebig University |
Iniguez Luy F.L.,Agri Aquaculture Nutritional Genomic Center
Plant Breeding | Year: 2012
High-throughput genomics technologies today offer unprecedented possibilities for gene discovery, complex trait analysis by genome-wide association studies, global gene expression analyses, genomic selection and predictive breeding strategies. Dissection of the complex Brassica napus genome using mapping-by-sequencing techniques provides a powerful bridge between genetic maps and genome sequences. The completed sequence of the Brassica rapa A genome and the expected forthcoming publication of the C genome (Brassica oleracea) will greatly accelerate the release of public reference sequences for B. napus (genome AC). Dramatically falling DNA costs for targeted or genomic resequencing and the availability of a new, high-density B. napus single-nucleotide polymorphism (SNP) array open the way for considerably more efficient mining and exploitation of genetic variation within the primary and secondary gene pools of B. napus. In this review, we outline some of the most significant recent advances in high-throughput genomics of Brassica crops and their potential impact on germplasm development and breeding of oilseed rape and canola in the coming years and decades. © 2012 Blackwell Verlag GmbH.
PubMed | Agri aquaculture Nutritional Genomic Center
Type: Journal Article | Journal: TAG. Theoretical and applied genetics. Theoretische und angewandte Genetik | Year: 2010
Publicly available genomic tools help researchers integrate information and make new discoveries. In this paper, we describe the development of immortal mapping populations of rapid cycling, self-compatible lines, molecular markers, and linkage maps for Brassica rapa and B. oleracea and make the data and germplasm available to the Brassica research community. The B. rapa population consists of 160 recombinant inbred (RI) lines derived from the cross of highly inbred lines of rapid cycling and yellow sarson B. rapa. The B. oleracea population consists of 155 double haploid (DH) lines derived from an F1 cross between two DH lines, rapid cycling and broccoli. A total of 120 RFLP probes, 146 SSR markers, and one phenotypic trait (flower color) were used to construct genetic linkage maps for both species. The B. rapa map consists of 224 molecular markers distributed along 10 linkage groups (A1-A10) with a total distance of 1125.3 cM and a marker density of 5.7 cM/marker. The B. oleracea genetic map consists of 279 molecular markers and one phenotypic marker distributed along nine linkage groups (C1-C9) with a total distance of 891.4 cM and a marker density of 3.2 cM/marker. A syntenic analysis with Arabidopsis thaliana identified collinear genomic blocks that are in agreement with previous studies, reinforcing the idea of conserved chromosomal regions across the Brassicaceae.